Using strand displacing polymerase to program chemical reaction networks.

@article{Shah2020UsingSD,
  title={Using strand displacing polymerase to program chemical reaction networks.},
  author={Shalin Shah and Jasmine Wee and Tianqi Song and Luis Ceze and Karin Strauss and Yuan-Jyue Chen and John H. Reif},
  journal={Journal of the American Chemical Society},
  year={2020}
}
Chemical reaction networks (CRNs) provide a powerful abstraction to formally represent complex biochemical processes. DNA provides a promising substrate to implement the abstract representation (or programming language) of CRNs due to its programmable nature. Prior works that used DNA to implement CRNs either used DNA-only systems or multi-enzyme DNA circuits. Architectures with DNA-only components had the rationale of being biologically simple systems. Multi-enzyme systems, on the other hand… 
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References

SHOWING 1-10 OF 28 REFERENCES
Enzyme-free nucleic acid dynamical systems
TLDR
The creation of a biochemical oscillator that requires no enzymes or evolved components, but rather is implemented through DNA molecules designed to function in strand displacement cascades is described.
Dynamic DNA-toolbox reaction circuits: a walkthrough.
TLDR
This paper defines a set of in vitro, DNA-based molecular transformations that can be linked to each other in such a way that the product of one transformation can activate or inhibit the production of one or several other DNA compounds, and shows how these reactions can be wired in arbitrary networks.
Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase
TLDR
A new DNA logic circuits architecture based on single-stranded logic gates and strand-displacing DNA polymerase requires less computation time and fewer DNA strands.
Programmable chemical controllers made from DNA.
TLDR
This work implements several building-block reaction types and combines them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.
Programmable autonomous synthesis of single-stranded DNA
TLDR
The concept of Primer Exchange Reaction (PER) cascades are introduced, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal processing, and actuation capabilities.
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA
TLDR
A design strategy is introduced that allows a specified input oligonucleotide to catalyze the release of a specified output oligon nucleotide, which in turn can serve as a catalyst for other reactions, which provides an amplifying circuit element that is simple, fast, modular, composable, and robust.
DNA as a universal substrate for chemical kinetics
TLDR
It is shown that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions, by using strand displacement reactions as a primitive, and systems implementing feedback digital logic and algorithmic behavior are illustrated.
Control of DNA strand displacement kinetics using toehold exchange.
TLDR
This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.
Improving the Performance of DNA Strand Displacement Circuits by Shadow Cancellation.
TLDR
Shadow cancellation is presented, a general-purpose technique to mitigate leak in catalytic DNA strand displacement circuits that makes no modifications to the underlying amplifier circuit and is agnostic to its leak mechanism.
Programming DNA-Based Biomolecular Reaction Networks on Cancer Cell Membranes.
TLDR
Compared to prior work of DNA circuits for evaluating cell membrane receptors, the DNA circuits by the architecture introduced have several major advantages including simpler design, lower leak, lower cost, and higher signal-to-background ratio.
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